Save intermediate outputs

[lucsanara]

Hello!

I have been running BASIL for a while, and I was wondering how to avoid automatic intermediate files deletion.

Best regards,
Lucía

[ellarowsthorn]

Hi Lucía,

I'm also a user of BASIL and have found adding the --debug flag at the command line does the trick, including keeping the tmp_asl_reg files instead of deleting them.

During processing they are stored in '/tmp/fsl_[process_id]_ox_asl', but with the --debug flag they will be moved to your output directory after completion.

Alternatively, if you're only looking to visually inspect some of the key intermediate files, running with the --qc-output flag would probably suffice and is a tidier option.

Best regards,
Ella

[lucsanara]

Hi Ella!

Thanks for your answer, it solved my question